We generalize the explicit high-order positivity-preserving entropy-stable spectral collocation schemes developed in [30, 34] for the three-dimensional (3D) compressible Navier Stokes equations to a time implicit formulation. The time derivative terms are discretized by using the first- and second-order implicit backward difference formulas (BDF1 and BDF2) that are well suited for solving steady-state and time-dependent viscous flows at high Reynolds numbers, respectively. The nonlinear system of discrete equations at each physical timestep is solved by using a dual time-stepping technique. The proposed scheme is provably entropy-stable and positivity-preserving and provides unconditional stability properties in the physical time. Numerical results demonstrating accuracy and positivity-preserving properties of the new dual time-stepping scheme are presented for supersonic viscous flows with strong shock waves and contact discontinuities.